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cufflinks

Transcript assembly, differential expression and regulation for RNA-Seq

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
Homepage:
Package version:1.3.0-2
Architecture:amd64
Distribution:Debian
Filename:cufflinks_1.3.0-2_amd64.deb

/usr/share/doc/cufflinks/README

CUFFLINKS
----------------------------
Cufflinks is a reference-guided assembler for RNA-Seq experiments. It
simultaneously assembles transcripts from reads and estimates their relative
abundances, without using a reference annotation.  The software expects as 
input RNA-Seq read alignments in SAM format (http://samtools.sourceforge.net).

Here's an example spliced read alignment record:
s6.25mer.
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/usr/share/man/man1/compress_gtf.1.gz

COMPRESS_GTF:(1)            User Commands           COMPRESS_GTF:(1)



NAME
       compress_gtf: - compress_gtf

SYNOPSIS
       compress_gtf   [options]  <reference.gtf>  <compressed_referÔÇÉ
       ence.gtf>

OPTIONS
       -r/--reference-seq                          reference   fasta
       file                     [ default:   NULL ]

       -F/--raw-fpkm                          use  FPKM  i
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/usr/share/man/man1/cuffcompare.1.gz

CUFFCOMPARE(1)              User Commands             CUFFCOMPARE(1)



NAME
       cuffcompare - helps analyze the transfrags

SYNOPSIS
       cuffcompare  [-r  <reference_mrna.gtf>]  [-R]  [-T]  [-V] [-s
       <seq_path>]

              [-o <outprefix>] [-p <cprefix>] {-i <input_gtf_list> |
              <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}


DESCRIPTION
       Cuffcompare  provides  cl
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/usr/share/man/man1/cuffdiff.1.gz

CUFFDIFF:(1)                User Commands               CUFFDIFF:(1)



NAME
       cuffdiff - find 
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/usr/share/man/man1/cufflinks.1.gz

CUFFLINKS:(1)               User Commands              CUFFLINKS:(1)



NAME
       cufflinks - Tran
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/usr/share/man/man1/cuffmerge.1.gz

CUFFMERGE(1)                User Commands               CUFFMERGE(1)



NAME
       cuffmerge - Merg
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/usr/share/man/man1/gffread.1.gz

GFFREAD(1)                  User Commands                 GFFREAD(1)



NAME
       gffread - one of
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/usr/share/man/man1/gtf_to_sam.1.gz

GTF_TO_SAM:(1)              User Commands             GTF_TO_SAM:(1)



NAME
       gtf_to_sam: - GT
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